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Entry version 68 (26 Feb 2020)
Sequence version 1 (23 Jan 2007)
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Protein

3-hydroxy-D-aspartate aldolase

Gene

bhcC

Organism
Paracoccus denitrificans (strain Pd 1222)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Catalyzes the condensation of glyoxylate and glycine into (2R,3S)-beta-hydroxyaspartate ((3S)-3-hydroxy-D-aspartate). Is essential for the growth of P.denitrificans in the presence of glycolate and glyoxylate since it functions in glyoxylate assimilation via the beta-hydroxyaspartate cycle (BHAC). Is also able to catalyze the reverse reaction in vitro, i.e. the cleavage of (3S)-3-hydroxy-D-aspartate, and that of D-threonine to a lesser extent.1 Publication

Miscellaneous

The beta-hydroxyaspartate cycle (BHAC) consists of BhcA, BhcB, BhcC, and BhcD enzyme activities. Overall, it converts two molecules of glyoxylate (C2) into oxaloacetate (C4) without the loss of carbon as CO2, under consumption of just one reducing equivalent and regeneration of the catalytic amino donor, which makes it one of the most efficient glyoxylate assimilation pathways. This cycle is of ecological importance in the assimilation of phytoplankton-derived dissolved organic carbon in marine environments by marine Proteobacteria, and suggests a trophic interaction between autotrophic phytoplankton and heterotrophic bacterioplankton. Oxaloacetate formed in the BHAC can directly enter the tricarboxylic acid cycle or serve as substrate for anabolic reactions.1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Protein has several cofactor binding sites:

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

kcat is 91 sec(-1) for the condensation of glyoxylate and glycine. kcat is 33 sec(-1) for the cleavage of (3S)-3-hydroxy-D-aspartate. kcat is 76 sec(-1) for the cleavage of D-threonine into acetaldehyde and glycine (PubMed:31723261).1 Publication
  1. KM=0.23 mM for glyoxylate1 Publication
  2. KM=4.31 mM for glycine1 Publication
  3. KM=0.28 mM for (3S)-3-hydroxy-D-aspartate1 Publication
  4. KM=9.24 mM for D-threonine1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei85Pyridoxal phosphate1 Publication1
    Binding sitei238Pyridoxal phosphate1 Publication1
    Binding sitei265Pyridoxal phosphate1 Publication1
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi355Magnesium1 Publication1
    Metal bindingi357Magnesium1 Publication1

    <p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

    <p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

    Molecular functionLyase
    LigandMagnesium, Metal-binding, Pyridoxal phosphate

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    PDEN318586:G1GW1-4573-MONOMER

    <p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
    Recommended name:
    3-hydroxy-D-aspartate aldolase1 Publication (EC:4.1.3.411 Publication)
    Alternative name(s):
    beta-hydroxyaspartate aldolase1 Publication
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
    Name:bhcC1 Publication
    Ordered Locus Names:Pden_3919Imported
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiParacoccus denitrificans (strain Pd 1222)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri318586 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeParacoccus
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
    • UP000000361 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 2

    <p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

    <p>This subsection of the 'Pathology and Biotech' section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

    Abolishes growth on glycolate or glyoxylate, but the deletion mutant strain is still able to grow on acetate, succinate or glucose with comparable growth rates as for the wild type.1 Publication

    <p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00004491001 – 3873-hydroxy-D-aspartate aldolaseAdd BLAST387

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'PTM / Processing' section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei62N6-(pyridoxal phosphate)lysine1 Publication1

    Proteomic databases

    PRoteomics IDEntifications database

    More...
    PRIDEi
    A1B8Z1

    <p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

    <p>This subsection of the 'Expression' section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

    Induced by glycolate.1 Publication

    <p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

    <p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

    Homodimer.

    1 Publication

    Protein-protein interaction databases

    STRING: functional protein association networks

    More...
    STRINGi
    318586.Pden_3919

    <p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

    3D structure databases

    SWISS-MODEL Repository - a database of annotated 3D protein structure models

    More...
    SMRi
    A1B8Z1

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    Protein Data Bank in Europe - Knowledge Base

    More...
    PDBe-KBi
    Search...

    <p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni256 – 257Pyridoxal phosphate binding1 Publication2

    <p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

    Belongs to the DSD1 family.Curated

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    ENOG4105E6Y Bacteria
    COG3616 LUCA

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    CLU_031639_2_0_5

    KEGG Orthology (KO)

    More...
    KOi
    K18425

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    RGGIKDV

    Family and domain databases

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    2.40.37.20, 1 hit
    3.20.20.10, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR001608 Ala_racemase_N
    IPR026956 D-ser_dehydrat-like_dom
    IPR042208 D-ser_dehydrat-like_sf
    IPR029066 PLP-binding_barrel

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF01168 Ala_racemase_N, 1 hit
    PF14031 D-ser_dehydrat, 1 hit

    Simple Modular Architecture Research Tool; a protein domain database

    More...
    SMARTi
    View protein in SMART
    SM01119 D-ser_dehydrat, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF51419 SSF51419, 1 hit

    <p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

    A1B8Z1-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MNAKTDFSGY EVGYDIPALP GMDESEIQTP CLILDLDALE RNIRKMGDYA
    60 70 80 90 100
    KAHGMRHRSH GKMHKSVDVQ KLQESLGGSV GVCCQKVSEA EAFARGGIKD
    110 120 130 140 150
    VLVTNEVREP AKIDRLARLP KTGATVTVCV DDVQNIADLS AAAQKHGTEL
    160 170 180 190 200
    GIFVEIDCGA GRCGVTTKEA VVEIAKAAAA APNLTFKGIQ AYQGAMQHMD
    210 220 230 240 250
    SFEDRKAKLD AAIAQVKEAV DALEAEGLAP EFVSGGGTGS YYFESNSGIY
    260 270 280 290 300
    NELQCGSYAF MDADYGRIHD AEGKRIDQGE WENALFILTS VMSHAKPHLA
    310 320 330 340 350
    VVDAGLKAQS VDSGLPFVYG RDDVKYIKCS DEHGVVEDKD GVLKVNDKLR
    360 370 380
    LVPGHCDPTC NVHDWYVGVR NGKVETVWPV SARGKGY
    Length:387
    Mass (Da):41,786
    Last modified:January 23, 2007 - v1
    <p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i831CE7FF51A8F0CA
    GO

    Sequence databases

    Select the link destinations:

    EMBL nucleotide sequence database

    More...
    EMBLi

    GenBank nucleotide sequence database

    More...
    GenBanki

    DNA Data Bank of Japan; a nucleotide sequence database

    More...
    DDBJi
    Links Updated
    CP000490 Genomic DNA Translation: ABL71985.1

    NCBI Reference Sequences

    More...
    RefSeqi
    WP_011750152.1, NC_008687.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    ABL71985; ABL71985; Pden_3919

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    pde:Pden_3919

    <p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

    <p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    CP000490 Genomic DNA Translation: ABL71985.1
    RefSeqiWP_011750152.1, NC_008687.1

    3D structure databases

    Select the link destinations:

    Protein Data Bank Europe

    More...
    PDBei

    Protein Data Bank RCSB

    More...
    RCSB PDBi

    Protein Data Bank Japan

    More...
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    6QKBX-ray1.70A/B1-387[»]
    SMRiA1B8Z1
    ModBaseiSearch...
    PDBe-KBiSearch...

    Protein-protein interaction databases

    STRINGi318586.Pden_3919

    Proteomic databases

    PRIDEiA1B8Z1

    Genome annotation databases

    EnsemblBacteriaiABL71985; ABL71985; Pden_3919
    KEGGipde:Pden_3919

    Phylogenomic databases

    eggNOGiENOG4105E6Y Bacteria
    COG3616 LUCA
    HOGENOMiCLU_031639_2_0_5
    KOiK18425
    OMAiRGGIKDV

    Enzyme and pathway databases

    BioCyciPDEN318586:G1GW1-4573-MONOMER

    Family and domain databases

    Gene3Di2.40.37.20, 1 hit
    3.20.20.10, 1 hit
    InterProiView protein in InterPro
    IPR001608 Ala_racemase_N
    IPR026956 D-ser_dehydrat-like_dom
    IPR042208 D-ser_dehydrat-like_sf
    IPR029066 PLP-binding_barrel
    PfamiView protein in Pfam
    PF01168 Ala_racemase_N, 1 hit
    PF14031 D-ser_dehydrat, 1 hit
    SMARTiView protein in SMART
    SM01119 D-ser_dehydrat, 1 hit
    SUPFAMiSSF51419 SSF51419, 1 hit

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    Search...

    <p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

    <p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiBHCC_PARDP
    <p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: A1B8Z1
    <p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 26, 2020
    Last sequence update: January 23, 2007
    Last modified: February 26, 2020
    This is version 68 of the entry and version 1 of the sequence. See complete history.
    <p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    <p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

    Keywords - Technical termi

    3D-structure, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
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